The Who, What, When, Where and Why of Chemistry
Chemistry is not a world unto itself. It is woven firmly into the fabric of the rest of the world, and various fields, from literature to archeology, thread their way through the chemist's text.
A hot object can transfer heat to its surroundings by conduction and convection, in other words by having molecules (or atoms) in the surroundings collide with the surface of the object, pick up some of its energy and move off. Imagine a little bucket brigade, stepping up to the object, grabbing a piece of heat (energy, really) and heading off to dump it elsewhere. Air doesn't conduct heat very well, and trapping it reduces convection (the bulk movement of the air - air currents), hence trapped air is an effective insulator.
If you halt the bucket brigade - prevent any molecules from walking off with a chunk of energy, all the energy stays in the object and voila my cocoa stays hot. So if I could envelop my cocoa in a bubble of nothingsness — a vacuum — I could keep it from cooling via conduction and convection. (Of course, I'd have to put a vacuum tight lid on the thing, lest it instantly boil off — but that's another post…) A convenient way to do this is to use a vacuum flask, where a 'layer' of vacuum is enclosed between two walls. Originally glass walls were used. If you're my age, you might remember dropping your lunch box, and then opening your thermos at lunch to find shard of glass inside. These days stainless steel or plastic walls make lugging your milk to school a less risky proposition.
Chemists still use the glass walled version of a thermos. We call it a Dewar (for James Dewar, who invented the contraption in 1892).
But an object untouched by other molecules can still lose heat by radiation, by emitting infrared photons - light at wavelengths longer than visible light. Reflective wrappings, like metalized Mylar, keep the light - and the warmth - inside.
A friend recently wondered why clear weather was cold weather. The earth radiates some of its heat back out into the universe as infrared radiation. Clouds act as insulating wraps for the earth, the water molecules grabbing the heat before it radiates out into space and re-emitting some of it back toward the planet's surface. (This is the greenhouse effect — it's not up for debate.) On a clear night, no clouds, so less heat is retained. Suddenly the temperatures are well below freezing.
(Other molecules besides water help trap infrared radiation within the atmosphere, including carbon dioxide and methane.)
The anatomy of a scientific paper. What do scientists mean when we say "the literature" (in hushed reverent tones)? What role does it play? Is a journal article as formulaic as a romance novel? Is this a bad thing? Where is the drama packed into a scientific paper? The introduction? The conclusion? Or are articles (as one of my students put it) "stripped of all their drama"?
Writing prompt of the day
Pick one of the titles below and write an introduction to this paper. If you don't know the meaning of a particular term, create a meaning. Five minutes.
• Kinetic Isotope Effects for the Reactions of Muonic Helium and Muonium with H2 • Enhanced lithium depletion in Sun-like stars with orbiting planets • One small step for a mouse • Transient Hoogsteen base pairs in canonical duplex DNA
What sets the tone in an article? Grab a journal article at random and start circling all the qualifiers - are they "needless words" (as William Strunk of Elements of Style fame would have it) or careful bounding on the part of the authors as to their claim?
Yes, the is an article, but "the article" is considered by many to be the best, the most important, the only way to communicate about science (at least to other scientists). Yes? No?
Who should be writing about science? What kinds of writing about science constitute scientific communication? Who should be writing them?
Writing prompt "All I want is a proper cup of coffee, made in a proper copper coffee pot." —Trout Fishing in America
Describe how your perfect cup of coffee is made. Start where you wish - with the beans, or with pouring it from a pot, or buying it at a cafe. Be specific and detailed. Don't drink coffee? (I don't!) Do the same with tea or hot chocolate or a favorite sandwich. Five minutes.
Alternate: Pick a routine prep you do in lab. Describe the perfect process. Be specific and detailed. Five minutes.
Next up The anatomy of a scientific paper: what does one of those all important journal articles look like?
We're covering density in my introductory chemistry this week - which prompted this post.
Density is the ratio of mass to volume and often (though not always) one of the easiest physical properties of a substance to measure. Introductory chemistry labs often feature an exercise where the mass of an object is determined using an analytical balance or somesuch and the volume is determined by displacement (often in a graduated cylinder).
In certain of my teen-aged sons' circles it's in fashion to write in public - to take your notebook (computer or spiral bound) and head to the local coffee shop. You can write the scene while being seen. Personally, I write in public as a last resort. Last week, while waiting to meet a friend for coffee I did haul out my iPad to see if I could inhale some of the fumes of caffeine and inspiration wafting around and some first thoughts for a column hammered out. No coffee for me, hot chocolate - with a serious mound of whipped cream on top.
While I'm all for decadence when it comes to chocolate, hot or otherwise, the whipped cream was a practical touch. My friend is notoriously late, and I wanted the chocolate to stay hot until he arrived.
The ability of a material to conduct thermal energy - heat - depends to some extent on its density. On a molecular level, heat transfer is mostly about collisions between molecules. If you are a molecule with lots of thermal energy, you are generally stuck with it all until you collide with another molecule!
Air at 20oC (68oF) feels warm (yes, I know it's about 3oC here right now, but a girl can dream, can't she?) while water at the same temperature feels refreshingly cool. Water is about a thousand times denser than air, so there are many more molecules in contact with your body surface. The more molecules boucing off a surface, the more opportunities there are for energy transfer. If you're hot, you'll get cooler faster by fully immersing yourself than by standing in a cool room. Conversely, if you want something to stay hot, surround it with air, not water. Air is a good thermal insulator, relative to water, because it is far less dense.
The whipped cream atop my hot chocolate is full of air, which lowers the density and so it floats on top of the cocoa. Heat transfer to the airy cream isn't very efficient due to the low density. Since the air trapped inside the cream isn't moving around (and thereby not presenting fresh molecules to take away the energy presently in the liquid in my cup), the system quickly equilibrates, with most of the heat in the system staying there.
Trapped air (or other gas) is a great insulator, but trapped nothingness works even better. Put my cocoa into a vacuum chamber and it should stay nice and toasty (though there would be other complications - but that is another post!).
Writing prompt Day 3: Pen or pencil? What is your preferred tool for writing by hand? Why? Describe your ideal pen or pencil, weight, ink, color, thickness, material. Expound on your preferences - why is a blue ballpoint infinitely preferable to a black marker? Five minutes.
Writing prompt Day 2 Pick one of the objects on the table and write a detailed description of it. You may handle the pieces. If you know the generally accepted name of the object, do not use it in your description. Either way, make up a name for the object.
Assorted questions on the table
What sorts of editing happen as notes get written? (Everything from the decision to pick up a pen or not -- if it means stripping off your gloves, or mucking up a pen, reliance on memory, distractions of running experimental work, your perspective/focus came up.)
David Everett suggests exercises for finding your voice - do real writers do things like this? Natalie Goldberg suggests writing without stopping for a set period. (Do real writers 'practice'? How? Why? What might you get out of exercises like these?)
How are new scientific terms birthed?
Writing along with us? Willing to share? Leave a link in the comments!
The first topic on the table in the new course I'm teaching is Field Notes, but I'm also hoping to use this space as my own field notes on the course and for responses from those of you "in the field" (writing, reading, blogging, practicing science). If you want to follow along - or better yet kibbitz - I'm posting the writing prompts that start off every class, some of the writing assignments and the readings.
Writing Prompt Day 1 Tell me everything you know about Jello. 5 minutes. Start.
Writing Assignment Make a transect. Map out a linear route and then make a detailed record of what you encounter along that route. The route can be long or short, indoors or out.Be imaginative. Examples: a transect across your room, on Merion green, across a microscope slide, a lab bench top, a parking lot. You can focus on a specific element in your transect, such as plant life, bacteria, or debris. If you chose to transcribe your notes (as Darwin did), attach the originals. Your notes should be roughly 300-400 words.
Questions I think it would be interesting to think about Are field notes/lab notebooks completely objective records of what was observed? Do they affect the science going forward? Is it ok to be vivid and "over the top" in field notes? Do they have to be linear? in pen? Why do think scientists rarely "get it right" in keeping notes? (Or at least that's what E. Bright Wilson thought.)
Readings for the first week:
First Thoughts, from Goldberg, Natalie. Writing Down the Bones: Freeing the Writer Within. Shambhala, 2005.
Beginner's Mind, Pen and Paper, Goldberg, Natalie. Writing Down the Bones: Freeing the Writer Within. Shambhala, 2005.
Notebooks and Records in E.B. Wilson in An Introduction to Scientific Research, Dover, 1991.
Trouble with the Editor, from Goldberg, Natalie. Writing Down the Bones: Freeing the Writer Within. Shambhala, 2005.
Introduction, from Strunk, William, and E. B. White. The Elements of Style, Fourth Edition.
Find a Voice and a Style, David Everett in Blum, Deborah, Mary Knudson, and Robin Marantz Henig. A Field Guide for Science Writers: The Official Guide of the National Association of Science Writers. Oxford University Press, USA, 2005.
The Open Sea (excerpt), Alister Hardy in Dawkins, Richard. The Oxford Book of Modern Science Writing. Oxford University Press, USA, 2008.
Complete collection of Linus Pauling's lab notebooks from Special Collections at Oregon State University.
Starting next week I'm teaching a new course called "Writing Science" -- a seven week exploration of the many ways science moves out of the lab or the field and into the wider world and what writing might have to do with such translations.
On the table are questions such as: How is science transformed as it moves out from the lab and the field into the broader scientific and lay communities? What gets lost (or found) in the translation from an article couched in equations and technical terms to an article in the Times or Discover? Who should be writing about science, or perhaps we should ask who's writing we should be reading? Is there a role in "official" (or "serious" or "real" or "scholarly", pick your adjective) science circles for "unofficial" channels like blogs and videos (the marvelous dance your Ph.D. thesis contest comes to mind!)?
We're reading and writing many genres - including: lab and field notes, the scholarly literature, things short and sweet (abstracts, tweets, radio spots, podcasts, blogs), science journalism, essays, humor, fiction, drama, poetry, and the visual.
The reading list is a work in progress, but if you want to follow along, I'll be posting each week's readings and writing prompts here - and some of the writing from willing participants. Illustration is a bit from Linus Pauling's lab notebooks. The entire set is digitized and available through Oregon State University's library here.
I took a fall skiing last week1, my skis went in one direction, my knees in the other. The audible pop sounded and felt much like what happens when I break the cartilage in the joint of a chicken. Argh.
Not surprisingly my knee hurts (though it's not all that swollen compared to the time I tore the ligament in my ankle, where the swelling was quite spectacular). I'm taking ibuprofen for the pain. NSAIDs, such as aspirin, naproxen, and ibuprofen are effective antinociceptives2 - painkillers. But I'm also adding a dollop of caffeine to each dose. It turns out that caffeine is an effective adjuvant for NSAID (non-steroidal anti-inflammatory drugs).
NSAIDs work by blocking the activity of prostaglandins, molecules that are used by the body in many signaling roles, including the signaling of pain. If the signal from my knee to the brain that says "pain" doesn't get through, it doesn't hurt (though it may still be hurt).
Adding around 100 mg of caffeine (roughly what's in my big mug of FTGFOP3 Assam tea) to 400 mg of ibuprofen makes it 2 to 3 times more effective in relieving acute pain. [Forbes et al.Clin Pharmacol Ther.1991 49(6):674-84.] Onset of pain relief is faster and the duration is markedly increased as well. Caffeine appears to increase the availability of the NSAID at the signaling site.
So sitting by the fire with a cup of tea (and an ice pack on my knee) is soothing in more ways than one...
1. Full disclosure: I fell in the lift line, my skis got entangled when I tried to retrieve the pole that got stuck in the snow. I'd love to say I did this catching an edge on a glorious powder run. 2. The word nociceptive was coined in 1904 by Charles Scott Sherrington to try to disentangle the psychological perception of pain from the physiological response. Noci- comes from the Latin nocere - to harm (think noxious and innocuous) 3. FTGFOP, Finest Tippy Golden Flowery Orange Pekoe, a description of the leaves, Orange Pekoe has nothing to do with any particular flavor of tea, including orange! 4. Food Research International Vol 29, Nos 3-4, pp. 325-330.